The infection and reservoir status of red squirrels (Sciurus vulgaris) for Borrelia burgdorferi sensu lato were studied in Switzerland. B. burgdorferi sensu lato was isolated from 15 skin samples from 4/6 dead red squirrels, victims of road traffic. Isolates were identified using restriction fragment length polymorphism (RFLP): B. burgdorferi sensu stricto was present in 14 culture tubes containing skin samples and B. afzelii in two other tubes. A mixed infection was revealed in one case. A total of 227 ticks attached to squirrels were cultivated in BSKII medium and 90 isolates were obtained. Genotypic identification by RFLP showed that B. afzelii (59%) and B. burgdorferi sensu stricto (46%) dominated in ticks feeding on red squirrels. Data collected from one particular animal, highly infested with Ixodes ricinus and harbouring numerous Borrelia-infected Ixodes ricinus ticks, showed that transmission of B. burgdorferi sensu lato occurred from S. vulgaris to feeding ticks. More precisely, B. burgdorferi sensu stricto and B. afzelii were mainly transmitted from S. vulgaris to ticks. The present data emphasized the results obtained previously from small rodents and birds in Japan and in Switzerland, showing the occurrence of specific associations between host species and Borrelia genospecies.